Our microbiome, the collection of microorganisms on and in our bodies, is important to our health. It also harbors opportunistic pathogens such as methicillin-resistant S. aureus (MRSA). Decolonization is a rapidly growing strategy to prevent MRSA infections fueled by new healthcare policy initiatives such as mandated surveillance cultures and public reporting of healthcare associated infections. Decolonization involves the application of targeted or non-targeted antimicrobials to the skin or mucosal surfaces. Given the role of our microbiome as a barrier to infection, decolonization regimens could have unintended negative consequences. Our preliminary microbial community profiling data suggests that Gram-negative bacilli (GNB) are part of the microbiome of the anterior nares, particularly in nursing home dwelling adults. A recent Cochrane meta-analysis showed that decolonization with intranasal mupirocin, a Gram-positive antimicrobial agent, increases the risk of infections due to organisms other than S. aureus including GNB. Gram-negative bacilli are increasingly multi-drug resistant and few novel antimicrobials are under development to treat them. Thus, interventions that shift infections from Gram-positive to Gram-negative pathogens could potentially have long term negative consequences for patients. In a clinical trial, we propose to study the microbiome of the anterior nares and posterior pharynx in populations with and without current exposure to the healthcare environment: (a) MRSA-colonized, community-dwelling adults and (b) MRSA-colonized, nursing home-dwelling adults. We will then compare the microbial communities at baseline and after a decolonization regimen of intranasal mupirocin and topical chlorhexidine within individuals in both populations. Our overall hypothesis is that the microbial composition of these sites and the response to decolonization vary by the living environment and that decolonization leads to re-colonization with an increasing proportion of Gram- negative bacilli. This proposal links a clinically important problem, the prevention of MRSA infections, with a novel methodology, microbial community profiling using high-throughout pyrosequencing of the 16S rRNA gene. Our short term goal is to determine if these increasingly used decolonization regimens targeted at controlling MRSA in particular may result in a secondary negative effect of promoting colonization with pathogenic Gram-negative bacilli. This would have an impact on the use of mupirocin for infection control purposes. The long term goal of this research is to use the information gained to develop novel intervantions to manipulate the human microbiome during healthcare to reduce the risk of MRSA infections with minimized negative consequences.